So I'm thinking, the farm is automated but it's not very good, you wouldn't get the output a normal farm would, but you'd be able to upgrade the equipment and make it better, but the best automated farm wouldn't out-produce the best manual one

Later in the game you get a greenhouse where you can grow crops year-round, including crops that continually produce from 1 planting. Not needing to regrow those plants every season and getting crops in winter absolutely increases output.

But the point of automation is to reduce time needed for farming so you can either increase how much os planted or do something else with your limited time